Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate 3607199 Dshi_0620 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Dino:3607199 Length = 250 Score = 100 bits (249), Expect = 3e-26 Identities = 81/261 (31%), Positives = 119/261 (45%), Gaps = 29/261 (11%) Query: 7 IAGKTVIVTGASSGIGKAIVDELLSLKVKVANFD-----LTDNGEKHENLLFQKVDVTSR 61 + KT +VTGA+ GIG A LL KVA D L + + + + DV+ Sbjct: 1 MTSKTAVVTGAARGIGLATTKLLLERGWKVAMIDRDGPALAEALQGLDGVHGIDCDVSDP 60 Query: 62 EQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQKGL 121 E VE +A + FG +DA+VNNAG+ D E A ++ + N G Sbjct: 61 EAVEGMIAETLREFGQIDALVNNAGV---------ADFGPIEETSFARWKTVMETNLDGP 111 Query: 122 YLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKYGV 181 +L QA L A K G ++N+AS +GL S + AY +KAAV T A ELG++G+ Sbjct: 112 FLCVQAATPALKATK-GAVVNIASISGLRASTLRVAYGTSKAAVIQLTLQQAVELGEHGI 170 Query: 182 RVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVADLV 241 R + PG + + +E + A PL R G E+A+ + Sbjct: 171 RANCVCPGPVRTKLAMAVHSQEIID--------------AYHDAIPLNRYGSEQEIAEAI 216 Query: 242 AYYISDRSSYITGITTNVAGG 262 + S+R+S+ITG GG Sbjct: 217 LFLCSERASFITGQVLAADGG 237 Lambda K H 0.313 0.131 0.361 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 150 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 266 Length of database: 250 Length adjustment: 24 Effective length of query: 242 Effective length of database: 226 Effective search space: 54692 Effective search space used: 54692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory